Metroid: Rise of Samus
by El Hustino
Summary: The Space Pirates ravage the galaxy unhindered, their power unstoppable. Will the galaxy's pleas and cries by answered by the birth of a miracle?
1. Prologue

A/N: Well, this'll be interesting. For quite a while now I have had a deep urge to write a Metroid-based piece of fanfiction. Since I have spent little time in the Metroid section, it may be odd not knowing what's cliché, overused or taboo, but I hope that I don't make any mistakes such as that in this story. I have also only played Metroid, Metroid: Zero Mission, Metroid Prime, and Metroid Fusion, so there may be a couple (hopefully not too many nor any too…ignorant) mistakes in this concerning the Metroid universe or timeline.

Also, this story in and off itself is of a slight AU, and will be concerning mostly with Metroid/Metroid: Zero Mission and anything before that, with a possible reach into the Metroid Prime area, but also will have things from a couple other of the games, so any mistakes there are in plot, will, most likely, be there purposefully.

Artistic license is fun, eh?

Oh, and as a warning I must say that there may be some…graphic scenes in this story. You can't have a galactic struggle and a war without fighting, bloodshed and death, right?

When reviewing (which I hope you will), please point out anything that you seem to see as a problem, no matter what it is. It would be very helpful.

* * *

**METROID**

**Prologue**

* * *

They were an ancient race, revered by all and hated by none, of which the galaxy had never seen the likes of before and most likely shall never witness the birth of another. Their technological breakthroughs eclipsed anything any other culture could possibly dream of and only their biological creations—little known by outsiders—were alone capable of making their technology seem even the slightest insignificant. What they were proudest of, though, was not some machine, living or metal, but their art. Wondrous feats of architectural design and amazing sculptures rivaling even the greatest artists of any other world or civilization.

They were the Chozo, a race as mysterious as they were impressive. For all their creations they kept to themselves for the most part, only venturing to visit—some say to study—other peoples and their worlds, sometimes leaving their grand temples and statues that they were so proud of amongst what many would call 'barbaric and underdeveloped' races compared to the them. They settled many worlds and left their marks upon countless others from one side of the galaxy to the other, including one unimportant blue and green planet in a system of nine others and a uninteresting average-sized yellow star. These temples would forever perplex the creatures that thrived upon the planets, making them constantly wonder where they came from, who created the great structures and, most importantly, why.

What made the Chozo so remarkable, even after taking in consideration all that they had done and were capable of, was their unwavering and awe-inspiring reverence for life. They cherished and loved all forms of life, childen in particular, and despite mastering hundreds of forms of battle and the fact that they must have been more than capable of immense destruction, the Chozo did all in their power to preserve every form of life they could, sometimes go as far as helping the more 'underdeveloped' sentient races. They surpassed every other in the universe immeasurably, why would they not help in tiny ways such as giving an insignificant piece of technology?

For hundreds of years, they, the great Chozo, lived and thrived, learning all they could about the galaxy and universe around them, mastering their art forms and sciences, leaving symbols of themselves across the galaxy as a reminder of their constant presence.

Now, though, those symbols are all that are left of their presence, for the Chozo, the most advanced culture in all of galactic history, disappeared. All that were left were the stone temples and the silent sentinels that were their statues. Many forgot they existed while others remembered the great teachers, as they were called on many a world. As time passed and other peoples grew and thrived, with or without the Chozo's past assistance, a great number dedicated their lives to researching their ancient history and attempt to unravel the mystery of their disappearance.

In the many years spent by thousands of archeologists from many different worlds, numerous theories came about. Some say another race destroyed the Chozo. To think anything capable of besting them in war, alone, was unusual thinking, but there was no proof of anything willing and able of something such as that….genocide on an immeasurable scale. Others say that they destroyed themselves, which was not something unusual for advanced beings to do, but the peaceful and caring Chozo? Few agree.

Still…others say that the Chozo are not gone. They are still alive, still around, watching the development of other races, learning out of pure curiosity and love for it, just as they always did, only now in secrecy, leaving their technology to become more apart of life itself. Of course, this is as much a theory as any of the others.

Whether dead or hiding, the fact is the Chozo are not willing to show themselves and have ceased interfering with any other culture in any way and taking their great presence with them, leaving a large hole in the galaxy, one that would have to be taken up by another intelligent form of life...

Sadly…this hole was, in fact, filled by another soon after the Chozo's disappearance…

Almost as brilliant and technological as the Chozo themselves, but as different as two sides of a coin, they cut a horrid swath of destruction throughout the galaxy. Moving like starved locusts, devouring dozens of planets' resources in relatively short time and committing genocide on a scale that was comparable to almost every war on every planet combined, they became synonymous with death and destruction, giving even the most hardened warrior nightmares. Their selfish disrespect for life was the exact opposite of the Chozo's, but was as deeply held and as great.

For a lack of a translated name, and due to their raid-like attacks on all vessels and planets, they have been coined the 'Space Pirates'. They are humanoid insects and act as one would expect of insects, constantly moving and using everything for as their own, and once they finish with a world, they move on, leaving nothing but a barren skeleton in the once fertile planet's place.

The Space Pirates, their weaponry and fighting skills comparable to even the Chozo's own, but lacking the Chozo's heart and spirit, have conquered innumerable worlds and peoples, and have killed off countless animals and creatures and hundreds of cultures, no matter how much resistance or hopeful negotiating was attempted.

All fall before their hunger and wrath, whether fighting to the end, wishing for mercy, or giving up themselves in hope for a quick ending.

It has come to light recently that the Chozo, before their disappearance, foresaw an incredible evil coinciding with their absence, leaving many to believe that they had knowledge of the Space Pirates, but were either unable or unwilling to stop them… But…the Chozo also foresaw a Great Defender, one that would rise in the face of such darkness and bring the galaxy to light, forever sending the evil back to the grim hole that it spawned from.

Whether true or false, the Chozo prophecies were little known and mostly ignored, while the areas of the galaxy that still thrived despite the Space Pirate onslaught, came together for the common goal of peace. Despite the grand quest and their courage, little progress has been made concerning the army of the Space Pirates. Many, many peoples have wished, hoped, prayed and begged for a miracle, possibly the return of the Chozo themselves, to halt the Space Pirates relentless and seemingly unstoppable conquest.

A Defender…A miracle…

On a little known planet in the far reaches of space, unknown to the rest of the more hurried and chaotic universe, a tiny miracle had been born…one's whose future was greater than anyone, even with the Chozo's art of prophecy, could possibly have imagined…


	2. Massacre of K2L

****

**METROID**

**Part One: The Rise of Samus**

* * *

**Chapter One: The Massacre of K-2L**

It was a tiny planet, nothing remarkable at first glance. It had forests here or there, many areas of rocky outcroppings, and a couple oceans, along with the other standard forms of land found upon habitable worlds. It had no natural intelligent life, only animals and other simple creatures, ones that live without thinking why it is that they live. Littered upon this seemingly unremarkable world were inspiring ruins of structures built by an ancient race long gone. Many planets had Chozo ruins, but few, if any, had them in this size and number.

The planet was covered with them, an amazing find! Amazing, for the archaeologists there, anyways. The sheer luck they had of finding such a world was comparable to a treasure hunter stumbling upon the tomb of a king. Soon after the news spread across the galaxy to those interested in such a thing, a colony made up of mostly archaeologists and other scientists along with a few others needed to support it. It was named K-2L, the simple label that the government gave it.

Among the many, many researchers was a family; a man and a woman, and their young daughter, a beautiful blonde child no more than four years old. The parents, Damien and Tessa, were the chief archaeologists of the mission, their knowledge of the bygone Chozo peoples making them necessary to accompany the other scientists, and they jumped at the chance to inspect such a find. That had been five years ago, and since then their daughter, Samus, had been conceived and born.

Making their way atop rocks, dirt, and rubble, the Aran family, with Damien in lead, excited to see for himself the great find one of the less experienced researchers had said they found, while Tessa, with tiny Samus clinging to her finger and walking beside her, did her best to keep up without actually running so that her daughter could keep up. The child ran as quickly as she could alongside her mother, her big blue eyes, the same as her mother's taking in all the gigantic rocks around her and her short blonde hair like her father's waved due to her running and the light wind. The path was almost a sheer cliff, and was difficult for them to traverse.

When they made it, finally, to the area of the find high atop the mountainside, they all were in awe…well, the parents were. Samus looked around while sucking on one of her fingers, oblivious to what her parents were so amazed by. In front of them, where there should have been more of the rocky outcropping that they had ran along the whole way there, was a gigantic area that had been smoothed into a wall, at least one hundred feet high and almost as wide.

"I always knew we should have built the colony further south," Damien said as he stared at the great hieroglyphs carved and painted on the smooth area. "We would have found things like this a lot sooner."

"Yes, but there's more ruins south, and we can't exactly put the colony on top of them," his wife pointed out, making him frown but nod in agreement. They moved closer to the stone wall, rubbing it with their hands, and leaving Samus close behind, who was doodling in the dirt with a stick. The wall was smooth, even after many years of suffering the planet's weather, and the images were still clear. "Besides, considering the geography around here, it's no surprise that this had stayed hidden for so long."

There were glyphs of Chozo priests in white garbs, their avian features obvious, all created to seem as if they were standing in a circle, for some sort of important ceremony. Around them were intricate etchings and designs. What interested the Arans the most, though, was the gigantic figure in the center. It stood from the bottom of the smooth area and ended near the top, the priests drawn around it, making it obvious that the center figure was of even more importance than they and that the ceremony, if that's what it was a depiction of, was centered around that specific Chozo. Other than being huge, the other thing that set it off was what it wore. The orange…armor, was it? They couldn't tell. Whatever it was, it was an orange, almost rust colored type of armor or clothing that covered the important Chozo's chest and head.

"Wow…that's…" Tessa began, "What is that? We've never seen anything depicting a Chozo in anything like battle gear or armor before."

Her husband shook his head, "I don't know. But that's our jobs, right? To figure all this stuff out?"

"Yes, you're right of course, but still," Tessa smiled, "This is…amazing, but we really should get back and have a team look around for more things like this." She looked around at the land around her. The tall craggy mountain face in front of her, the rocky ground behind going the entire way down the mountain and the tiny forest and grassy area farther off. Ruins could be found and had been found in every area they had looked in. "It's funny, everyday I can't help but be surprised that a place like Zebes would have anywhere near this number of ruins."

"That's why, I, everyday, think that we're lucky the miners looking for ore or whatnot stumbled onto it." The couple returned to their child, sitting on her butt, drawing in the dirt, her face and clothes a mess. They both smiled and the mother reached down to pick Samus up into her arms.

"So, Samus, what have you been drawing?" the little girl answered her mother by staring at her with her huge blue eyes and silently pointing down at the ground to make them look for themselves. There, four stick figures stood. One, tiny, was obviously Samus, the other two the parents recognized as themselves. The fourth, though…they were not sure about. Unlike the others, it had three long fingers and a thumb, was taller than the others, and had what they could only guess as a beak on its face.

The man grinned at his wife, "A Chozo. See, she is starting to get interested in our work."

The little blonde girl shook her head and pulled her finger out of her mouth, "It's the nice man I see. Helps me with stuff and does this," she wiggled her fingers in as if she was playfully greeting someone, "and says 'hi'. But you can't see him, 'cause he's 'fraid of you. He's hiding." She stuck her finger back into her mouth when she was finished talking, leaving the adults to stare at each other in confusion. At first they thought she had been doodling the glyphs they had been seeing all the time, but they had no idea what she was talking about.

They could only shrug at each other and told each other it must be some sort of imaginary friend. "Time to go back, Samus, you've had enough fun outside today." The girl pouted and her mother poked her on the nose, "Besides, you're as dirty as a little grizby and need a bath." The girl giggled. Tessa left carrying Samus in her arms, heading back to the colony.

Damien began to follow, but a sound distracted him, and he jumped in a circle, just in time to see what he thought was a talon with three fingers and a thumb disappear behind one of the craggy outcroppings. After staring for a moment, he decided it was his imagination coupled with a lack of sleep and bad coffee. But…he couldn't shake the feeling that something—some_one_—was there.

* * *

The hike to the colony complex was long, so it was no surprise to the family that the sun was past the horizon well before they returned and Samus had fallen asleep in her mother's arms. Tessa shifted her daughter's weight in her arms and looked over to her husband who seemed to be lagging behind, "What's the matter, Damien?"

Shaking his head as if pulling himself out of deep thought, the man smiled, "Oh, uh, nothing. I'm just thinking about the…ruins." He watched his wife give him a face that showed that she didn't believe that for a moment, but didn't bother to press any further. The scientist had been thinking, that was true, but his thoughts were on the figure he may or may not have seen. There had been odd…happenings lately, most of which involving Samus.

There have been times that the girl would be looking off away from everyone else, as if being distracted, giggling, but when one of the adults would turn, no one would be there. Another time, after realizing that Samus had wondered off during one of their digs in an area with many cliffs and crags, Tessa and Damien searched frantically, only to find their daughter when they returned to their small camp, curled up atop the table and covered with a blanket. Strangest were the shapes in the dirt near the table…Damien swore they were footprints of…something.

Stuck deep in thought again, Damien was jumped when his wife cried out later, "Damien, come quick!" The man quickly rushed to his wife, whose eyes stared forward in shock, "Look!" He quickly realized where they were: in his thoughts Damien didn't notice that they had reached the last tall hill before the colony. Even in the evening gloom, he could see that smoke rolled out of one area, a giant fire. Without saying anything to one another, the adult Arans ran towards the habitation, the tiny Aran still asleep.

Damien, not weighed down by carrying anything, made it to the entrance first. _Damn…the plasma drill better not have overloaded, _he screamed to himself. Once he input the code, the doors slid apart. He stepped in, "What's hap—" the smell that poured from the doors gagged him. He coughed and his eyes watered, but once the shock of just what the smell was sunk into him, the discomfort was the last thing he could think about. _Burnt…flesh…It smells like burnt flesh!_

Inside the hall were bodies, slouched against the wall, crumpled on the ground. Dead corpses of his colleagues, his friends, the people he was supposed to look after, being the head of the colony. Most of the people were burned beyond recognition and others missed limbs or whole sections of their bodies. The light fixtures dangled from the ceilings, flickering on and off, making the bodies cast shadows against the walls. The normally white and sterile walls were covered with black scorch marks and a dark ooze that they recognized as blood and gore.

"Oh…my…" Tessa said in a whisper, covering her mouth in shock. Damien clenched his fists and slammed one into a wall. "Who…What could have possibly done something like this? There's no wild animals near here that could do anything like this." Neither wanting to leave before they knew the answer, the husband and wife walked through the carnage, keeping their eyes away from the dead around them. Once, Samus began to whine, but Tessa shushed her, and the child quickly silenced, never waking up.

"Agh! No, leave me alone!" A voice shouted from somewhere ahead of them. They both had to squint to see through the darkness and faint smoke. A man came around a corner, sweating and his face flushed from running. When he noticed the Arans, he turned and ran to them as if they would be able to save him. "Damien! You came back!"

Damien grabbed the man's shoulders and looked him in the face, "What happened?!" The man's mouth opened and closed. His eyes shut and he looked away as tears welled up in his eyes. Whatever had happened, it had scared him to the point that he couldn't speak. "You need to tell me." The man looked back at Damien's pleading eyes, and opened his mouth.

Just as something slammed into the man's back and his eyes rolled up into his head. He slipped out of Damien's grip and fell to the ground, smoke and steam pouring from a crater in his back. Tessa screamed and jumped back, clutching Samus even tighter. Damien, mouth agape, looked away from his fallen friend to see what had done that to him.

Far…on the other side of the hall, stepped the creature that had been in pursuit of the now dead man. It was monstrous, its head almost reaching to the ceiling, which was at least three yards high. It had long, powerful legs supporting a giant torso that had two bulging arms that ended in deadly claws, all of which was covered in a charcoal-covered carapace. Each claw had a laser attached, one of which was smoking from its recent use on the scientist, but the humans knew that those were not its only weapons or means of killing. The eyes of the creature, small and faceted like a bug's, locked onto the family. The Space Pirate, with new targets, began moving towards them.

Not thinking of anything else other than his wife and daughter, Damien clutched Tessa's hand and dragged her into a nearby hall, just as a wave of neon green bolts shot through the air that they had occupied. The family ran, their daughter now awake and screaming from the excitement, and although Tessa did her best, Samus would not quiet down, as if she knew of the danger that pursued them.

Entering a crossing of two halls, Damien led his family into the left, skidding to a quick stop as he saw the backs of two more Space Pirates, one the same color as the first and the other a dark rusty red color. They turned, going in the opposite direction, the first Pirate firing at them as they past his vision, which got the attention of the other two. Tessa was now dragging her husband behind her, Samus still squalling in her arms. She found a doorway into another hall, and entered it. Damien quickly input an emergency code into the keypad nearby, and the heavy doors sealed shut.

"What…" Damien panted, "What would Space Pirates want with the colony?" Tessa did the best to comfort their daughter and only gave a sad shake of her head to show she had no idea. The sound of lasers hammering into the door followed by a pummeling and banging suddenly jumped the humans, who quickly took off before the aliens could tear down the door that was supposed to hold back intruders easily. Yes, most intruders would be at a dead end in front of one, but that which was impenetrable to others were nothing more than an inconvenience to the Space Pirates.

"The boiler room!," Damien shouted, "It has the heaviest doors in the entire complex and is right near here!"

"You're right, and they wouldn't expect us to hide, they'd expect us to try and get out," Tessa added. They headed in the direction of the boiler room, and made it there in little time, having to turn a number of corners, which gave them hope that the insectoid Space Pirates would lose them. The room was quite long and relatively empty, with the 'boiler', which was actually nothing more than a large computer and machine against one wall the regulated, not only temperature, but the air and gasses with the colony. Being such an important area, it was for high ranking personnel only and had a large armored door, much more durable than any of the other ones.

Damien shut and locked the door, and he huddled against the far opposite wall with his family, sitting between the large computer and a vent shaft. In the silence after, they could hear the steps of the creatures outside, although muffled from the door. Even Samus was silent, possibly sensing the fear that her parents radiated; she did not bother to ask them what it was they were hiding from or why it was chasing them.

Once they heard no more steps, Tessa and Damien let out their breath, neither realizing they were holding it. All they had to do, if they were lucky, was wait for the Space Pirates to take what they want and move on so that they could somehow call for help.

Sadly, as history has noted, their luck was not in their favor.

They soon heard more steps, but these did not continue, they stopped right in front of the door. The Arans waited, and soon the steps continued, but the relief it gave them was false. A great explosion rocked forth, tearing the door apart and filling that end of the room in thick smoke. Walking in by twos, six Space Pirates, three of the rusty red color, the charcoal one, and two more that were a midnight blackish blue. The latter were larger than the others and had the air of being commanders. The first four stood along the walls, two on each side, completely erect in honor of the commanders.

But…the commanding Pirates did not continue towards the Arans, they gave the humans a glare and acknowledged them, but looked away and stood along the wall in the same stance as the others. Damien, confused at the Space Pirates, who he heard to be erratic and mindless, now acting as if the leaders of the colony and probably the last people left alive were not there, just watched. He knew the midnight blue ones were the commanders, but they seemed to be waiting in honor, just as the others were, for someone…

Through the churning smoke, seeming to be born from it, stepped forth a creature that made even the Space Pirates seem like a gentler species. It was gigantic, almost filling up the height and width of the room completely, but moved with a sort of elegance that allowed it to now become crapped in the relatively small space. It had a long snout, a maw filled with innumerable teeth and a crooked neck similar to a vulture's own. It's body was pure muscle, but it was also lithe and was obviously built for not only power but speed and agility, as well. The arms were long and ended in huge talons, two long fingers and a thumb and the legs were long, the muscles taut. The creature was easily five yards long, but the whip-like tail, which ended in a spear, waved behind him, was another five or more. To compare it to any other creature one would have to take the ancient and long extinct dinosaur raptors that had preyed upon the primordial world of earth, but the giant wings that folded along its back gave it the appearance of a great, mythological beast found in hundred of cultures, on earth or otherwise.

A dragon.

The most fearful aspect of the beast was not its body, a body created for no other purpose than destruction and carnage, but its _eyes. _The eyes set in his head had both the beastly of a murderous predator, but also belayed its incredible intelligence, a creature that could destroy not only with its body, but also with its wit. Even thought Damien was not a biologist, he could still tell that this creature, whatever it was, dragon, dinosaur, or some nightmare from space, was the perfection of a predator.

The deep, dark purplish black dragon stepped forth towards the humans, its toothy mouth curved into a slight grin. The Space Pirates, as he walked by, lifted their claws across their chests in a salute and the monster screeched, a high-pitched rattling sound, as he walked by them. _Whatever…no, whoever this is, _Damien thought as the beast came closer, _he's not another one of the Pirates' creatures they use for weapons. _Anyone that had some sort of form of communication knew of the Space Pirates' love for creating and using beasts to use in their war, sometimes preferring them to machines.

Tessa clutched Samus to her chest, and Damien stood up, clearing his throat, legs shivering and his brow covered with sweat. One of the long, clawed fingers pointed towards the man. "You." Damien jumped back in shock as the dragon spoke English. Its voice still sounded slightly screechy, but his voice was quite clear. "You are Damien Aran?" He nodded. "Good, I've been looking for you, the commander of this colony, yes?"

"I—I—I'm not a commander, I just lead the research here…or I used to, before…" Damien dropped it there, not having the nerve nor the want to talk to the monster anymore.

"I only wanted to be sure that we had gotten each of you. Leave no survivors, I am sure you understand. I was hoping you were braver than the other trash and would tell us where we could find another of the plasma drills you must have."

"First of all," Damien's anger overrode his fear, "There was only one plasma drill, and you obviously were stupid enough to break that." As he spoke, Tessa's eyes grew in fear, but the dragon smiled and had a brow raised, as if amused. "Second of all, I wouldn't tell you scum _anything_!"

"Oh…I suddenly realized that I have not introduced myself." The creature stood as straight as he could in the room, spread his wings slightly, and whipped his tail, "I am Ridley, Commander of the Space Pirate Army."

Damien gasped. He had heard of Ridley, the commander of the Space Pirates' vast army. The stories of him had crossed from one side of the galaxy just as any about the Space Pirates had. Stories of a beast cunning enough to control the Space Pirates to victory in every battle he was in and of a monster that even the strongest Pirate would bow before.

Ridley wrapped one of his claws around Damien's torso and lifted him as if he was no more than a doll. "Now that I am aware that there are no more of those drills…there is nothing of use on this planet…other than the planet itself, of course. I was hoping to have a nice new weapon, but…" his face closed in on Damien's, their eyes close, but Ridley's head was as large as the man's body, "You must understand how upset this makes me." Damien glared in defiance, already aware of his fate.

"Go to Hell."

Ridley's grin grew, and Tessa watched as the dragon easy pushed the claw on his thumb through her husband's torso, leaving a whole large enough to put her arm through. She screamed his name, but he was dead before Ridley dropped him to the ground. The monster's gaze turned to her, but he lost his dark grin, "The fledgling…where is she?"

"Where is what?" Tessa's voice quivered, but she folded her empty arms and looked the Space Pirate Commander in the face.

"Your, your—Damn your language!—you know what I am speaking of! Where is it?" The predator was growing frustrated from losing such a small target. Tessa glared silently. Ridley placed his face into hers, his breath reeking, "Tell me where it is!" tears in her eyes, Tessa spat onto the giant beast's face. It was only a tiny droplet, but Ridley stepped away from her, and as he did so he noticed the vent shaft's cover was loose. With one great sweep of his hand, he knocked the woman into a wall, and she crumpled to the ground. He tore away the vent cover and tried to shove his snout into the hole, but it was much too small. He crouched down and placed his head next to it, and saw the tiny legs of a child scurrying around a corner in the vents.

Letting out a snarl and another shaking screech, Ridley turned to the Space Pirates that had stood still and silent during the whole situation. "It is no threat at all, but keep a squad here incase it or any other is found," Ridley said in his own screechy language. The Pirates, other than the two midnight blue commanders, ran off to comply. The two left followed Ridley as he left, licking the blood from his talon.

"Zebes is ours now, the Mother Brain will be pleased."

* * *

A/N: So, should I continue, or not? Hopefully it's not too bad, althought I've never read too much Metroid fanfiction. Althought I should...anyways, please tell me what you think in your review, since, ya know, that's what they're for.


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